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Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PXW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M MES pH6.5, 2.13M Lithium acetate
Crystal Properties Matthews coefficient Solvent content 2.69 54.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.811 α = 90 b = 81.811 β = 90 c = 232.957 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2015-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.11 46.59 100 0.998 14.4 14.3 27598
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.11 2.17 0.718
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.11 45.031 27509 1313 99.982 0.175 0.1736 0.1744 0.2125 0.214 30.084
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.06 0.03 0.06 -0.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.255 r_dihedral_angle_4_deg 17.308 r_dihedral_angle_3_deg 16.321 r_dihedral_angle_1_deg 7.972 r_lrange_it 6.497 r_lrange_other 6.455 r_scangle_it 4.048 r_scangle_other 4.047 r_mcangle_it 3.333 r_mcangle_other 3.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.255 r_dihedral_angle_4_deg 17.308 r_dihedral_angle_3_deg 16.321 r_dihedral_angle_1_deg 7.972 r_lrange_it 6.497 r_lrange_other 6.455 r_scangle_it 4.048 r_scangle_other 4.047 r_mcangle_it 3.333 r_mcangle_other 3.333 r_scbond_it 2.564 r_scbond_other 2.563 r_angle_refined_deg 2.15 r_mcbond_other 2.018 r_mcbond_it 2.016 r_angle_other_deg 1.505 r_symmetry_nbd_other 0.201 r_xyhbond_nbd_refined 0.2 r_symmetry_xyhbond_nbd_refined 0.199 r_nbd_other 0.193 r_nbd_refined 0.19 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.109 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.091 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2387 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing